Quantities

library(drake)
library(tidyverse)
loadd(model_data_with_na, model_data, imputed_data)

Look at NA values in raw data

map_int(model_data_with_na, ~sum(!is.na(.)))

##                               iso3c                        n_amr_events 
##                                 190                                  59 
##                  health_expend_perc              migrant_pop_per_capita 
##                                 184                                 190 
##                          population                       ab_export_bin 
##                                 190                                 162 
##                      english_spoken               human_consumption_ddd 
##                                 190                                  68 
##                       livestock_pcu                ab_export_per_capita 
##                                 164                                  87 
##                ab_import_per_capita livestock_consumption_kg_per_capita 
##                                 161                                  31 
##                      gdp_per_capita         tourism_outbound_per_capita 
##                                 190                                  44 
##          tourism_inbound_per_capita                 pubcrawl_per_capita 
##                                 111                                 180 
##          promed_mentions_per_capita 
##                                 189

model_data_with_na %>% 
  filter(pubcrawl_per_capita == 0 | is.na(pubcrawl_per_capita)) %>%
  nrow()

## [1] 33

model_data_with_na %>% 
  filter(promed_mentions_per_capita == 0 | is.na( promed_mentions_per_capita)) %>%
  nrow()

## [1] 1

model_data_with_na %>% 
  filter(ab_export_per_capita == 0 | is.na( ab_export_per_capita)) %>%
  nrow()

## [1] 103

Look at NA values and distributions post-NA processing

map_int(model_data, ~sum(!is.na(.)))

##                                  iso3c 
##                                    190 
##                           n_amr_events 
##                                    190 
##                     health_expend_perc 
##                                    184 
##              ln_migrant_pop_per_capita 
##                                    190 
##                          ln_population 
##                                    190 
##                          ab_export_bin 
##                                    162 
##                         english_spoken 
##                                    190 
##                  human_consumption_ddd 
##                                     68 
##                       ln_livestock_pcu 
##                                    164 
##                ln_ab_export_per_capita 
##                                    190 
##                ln_ab_import_per_capita 
##                                    161 
## ln_livestock_consumption_kg_per_capita 
##                                     31 
##                      ln_gdp_per_capita 
##                                    190 
##         ln_tourism_outbound_per_capita 
##                                     44 
##          ln_tourism_inbound_per_capita 
##                                    111 
##                 ln_pubcrawl_per_capita 
##                                    190 
##          ln_promed_mentions_per_capita 
##                                    190

map_lgl(model_data, ~any(is.infinite(.))) # confirm no infinite values

##                                  iso3c 
##                                  FALSE 
##                           n_amr_events 
##                                  FALSE 
##                     health_expend_perc 
##                                  FALSE 
##              ln_migrant_pop_per_capita 
##                                  FALSE 
##                          ln_population 
##                                  FALSE 
##                          ab_export_bin 
##                                  FALSE 
##                         english_spoken 
##                                  FALSE 
##                  human_consumption_ddd 
##                                  FALSE 
##                       ln_livestock_pcu 
##                                  FALSE 
##                ln_ab_export_per_capita 
##                                  FALSE 
##                ln_ab_import_per_capita 
##                                  FALSE 
## ln_livestock_consumption_kg_per_capita 
##                                  FALSE 
##                      ln_gdp_per_capita 
##                                  FALSE 
##         ln_tourism_outbound_per_capita 
##                                  FALSE 
##          ln_tourism_inbound_per_capita 
##                                  FALSE 
##                 ln_pubcrawl_per_capita 
##                                  FALSE 
##          ln_promed_mentions_per_capita 
##                                  FALSE

model_data %>%
  select(-iso3c, -n_amr_events, -english_spoken) %>%
  gather() %>%
  ggplot(aes(x = value)) +
  geom_histogram() + 
  facet_wrap(key~., scales = "free")

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

## Warning: Removed 595 rows containing non-finite values (stat_bin).

model_data %>%
  dplyr::select(-iso3c, -ln_livestock_pcu, -ln_ab_import_per_capita, -ab_export_bin, -english_spoken) %>%
  PerformanceAnalytics::chart.Correlation(., histogram = TRUE, pch = 19, method = "spearman")

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

Look at imputed data

plot(imputed_data) # On convergence, the different streams should be freely intermingled with one another, without showing any definite trends. Convergence is diagnosed when the variance between different sequences is no larger than the variance within each individual sequence.

show_imputes(imputed_data, m = imputed_data[["m"]], raw = model_data)

imp <- complete(imputed_data)
imp %>%
  dplyr::select(-iso3c) %>%
  PerformanceAnalytics::chart.Correlation(., histogram = TRUE, pch = 19, method = "spearman")

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties

## Warning in cor.test.default(as.numeric(x), as.numeric(y), method = method):
## Cannot compute exact p-value with ties